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Stacks

Introduction

From the Stacks web site:

"Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography".

Stacks on Breezy

Stacks 1.42, 1.44 and 1.46 have been installed on Breezy with default configuration options, except that sparsehash options have been included for performance enhancement. To use version 1.46 (and similarly for 1.42 and 1.44), add the following to your batch job script before running Stacks:

module load stacks/1.46

Older versions

Stacks 1.41 was installed on Breezy with only default configuration options.  To use this version, add the following to your batch job script before running Stacks:

module load stacks/1.41

Stacks 1.35 and many earlier versions have been built on Breezy without the web interface and without MYSQL support.  SAM tools and sparsehash options have been included for performance enhancement. The Spreadsheet:ExcelWriter Perl module was installed to allow output to Excel-format files. 

Current Stacks versions depend on some features of C++ that require a more recent compiler than the default on Breezy.  As shown below, a module to set up the run-time environment for this compiler must be loaded as part of the setup to use Stacks 1.35 (or similarly for earlier versions).  The Stacks binaries and Perl scripts have been installed to /global/software/stacks/stacks135/bin.  For a bash shell user add the following to your batch job script before running Stacks:

export PATH=/global/software/stacks/stacks135/bin:$PATH
module load perl_modules
module load gcc/gcc-4.9-20140406-beta

For More Information

Updated:
2013-11-26 - Stacks 1.09 notes.
2014-04-29 - Stacks 1.19 notes.
2014-12-04 - Updated for Stacks 1.21 .
2015-02-06 - Updated for Stacks 1.24.
2015-02-27 - Updated for Stacks 1.27.
2015-03-25 - Updated for Stacks 1.29.
2015-06-17 - Updated for Stacks 1.31.
2015-08-07 - Updated for Stacks 1.34.
2015-09-29 - Updated for Stacks 1.35 and removed Stacks 1.09 documentation as that was a special case that is likely no longer relevant.  Changed Stacks home page location.
2016-09-03 - Updated for Stacks 1.42 and 1.41.
2016-10-18 - Updated for Stacks 1.44.
2017-05-10 - Updated for Stacsk 1.46.